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ECRbase specifications

Information


Unique identifier OMICS_22198
Name ECRbase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/ECRbase

Maintainer


  • person_outline Ivan Ovcharenko

Publication for ECRbase

ECRbase citations

 (5)
library_books

Site specific programming of the host epithelial transcriptome by the gut microbiota

2015
Genome Biol
PMCID: 4404278
PMID: 25887251
DOI: 10.1186/s13059-015-0614-4

[…] lyses were performed based on GO annotation or regulatory factors. The transcription factor binding targets were retrieved and combined from the Cscan database [], including ChIP-Seq data [], and the ECRbase database []. The microRNA targets were retrieved and combined from TargetScan database [,] and miRanda database [,]. For each analyzed group of genes, their GO, transcription factor and microR […]

library_books

The Identification of Pathway Markers in Intracranial Aneurysm Using Genome Wide Association Data from Two Different Populations

2013
PLoS One
PMCID: 3590201
PMID: 23483893
DOI: 10.1371/journal.pone.0057022

[…] sense, frameshift, missense and 5′ and 3′-UTR designations), impact of an amino acid substitution on the properties of the protein product from PolyPhen server , , evolutionary conserved regions from ECRbase , and all possible LD proxies - SNPs with r2 over a predefined threshold in a specific HapMap sample . On the other hand, F-SNP score incorporates: functional effects of SNPs, predicted at the […]

library_books

Unique Alterations of an Ultraconserved Non Coding Element in the 3′UTR of ZIC2 in Holoprosencephaly

2012
PLoS One
PMCID: 3409191
PMID: 22859937
DOI: 10.1371/journal.pone.0039026

[…] on factors that controls DNA binding ability (data not shown); however, we also noted an extremely conserved element in the non-coding 3′ UTR. Two independent analysis procedures using EvoPrinter and ECRbase (http://ecrbase.dcode.org/) identified a comparable region of conservation in the ZIC2 3′UTR that spanned nearly 800 bp (). shows an expanded view of the conserved region that includes all kno […]

library_books

Genome wide survey of microRNA–transcription factor feed forward regulatory circuits in human† †Electronic supplementary information (ESI) available: Description of oligo analysis and randomizations for network motifs analysis, randomization results for the network motifs analysis of mixed feed forward loops, and supplementary files S1–S11. See DOI: 10.1039/b900177h Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file. Click here for additional data file.

2009
Mol Biosyst
PMCID: 2898627
PMID: 19603121
DOI: 10.1039/b900177h

[…] , and the miRBase, PicTar and TargetScan databases for the post-transcriptional ones. Let us see in more detail how we used these sources of information:• The Evolutionary Conserved Regions database (ECRbase) is a collection of evolutionary conserved regions, promoters and TFBSs in vertebrate genomes, based on genome-wide alignments created mainly with the Blastz program. Even if both our pipeline […]

library_books

Supplementing High Density SNP Microarrays for Additional Coverage of Disease Related Genes: Addiction as a Paradigm

2009
PLoS One
PMCID: 2668711
PMID: 19381300
DOI: 10.1371/journal.pone.0005225

[…] ccone and colleagues. The score incorporates a number of factors, including SNP/gene functional properties (such as coding and promoter regions), and evolutionary conserved regions (ECRs, provided by ECRbase , http://ecrbase.dcode.org). The original GIN method introduced by Saccone and colleagues incorporated LD into the prioritization score through the use of LD proxies. This is more appropriate […]


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ECRbase institution(s)
CMLS, Computation Directorates, Lawrence Livermore National Laboratory, Livermore, CA, USA
ECRbase funding source(s)
Supported by LLNL LDRD-04-ERD-052 grant, LLNL LDRD-06-ERD-004 grant and the United States Department of Energy by the University of California, Lawrence Livermore National Laboratory Contract W-7405-Eng-48.

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